chr11-1063767-T-C

Position:

• chr11-1063767-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001748091.2(LOC107987157):​n.566+25A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,806 control chromosomes in the GnomAD database, including 12,828 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.41 (12828 hom., cov: 31)
• Consequence: LOC107987157 XR_001748091.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.999

Genes affected

LOC107987157 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987157	XR_001748091.2	n.566+25A>G		intron_variant, non_coding_transcript_variant
LOC107987157	XR_007062544.1	n.591A>G		non_coding_transcript_exon_variant	4/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62042 AN: 151688 Hom.: 12807 Cov.: 31

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.420

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.409 AC: 62103 AN: 151806 Hom.: 12828 Cov.: 31 AF XY: 0.407 AC XY: 30167 AN XY: 74188

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.420

Alfa AF: 0.426 Hom.: 2974

Bravo AF: 0.395

Asia WGS AF: 0.433 AC: 1504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.20

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2301160; hg19: chr11-1063767;